# Two Channel Chemistry and Imaging on the MiSeq i100 Series

**Background**

The MiSeq i100 Series uses two-color chemistry, which allows for rapid imaging of the flow cell using blue and green fluorescent excitation channels at every sequencing cycle. The MiSeq i100 Series is powered by XLEAP-SBS chemistry, a faster, higher quality, and more robust update to Illumina's sequencing by synthesis (SBS) chemistry.

*Chemistry*

In two-channel chemistry, the base calls are assigned by the fluorescent excitation-emission spectra that are designated by that base. The MiSeq i100 Series uses the following designations:

* Clusters with intensity in **green** only: **T**
* Clusters with intensity in **blue** only: **C**
* Clusters with intensity in both channels: **A**
* Clusters with no intensity/dark: **G**

  ![](/files/ZHhruU5cAmgmGKVtuDcM)\
  ![](/files/Voe71UsRCcCog0WmLQJV)

*CMOS Flow Cell*

The MiSeq i100 Series uses a patterned flow cell with nanowells fabricated onto a CMOS chip.

![](/files/Dt32a4u9B1lURTru7dmC)

*Imaging Tiles*

5M: 1 lane x 9 swaths x 2 tiles = total of 18 tiles imaged.

![](/files/oKfHZSKcu5YEiCXSSUEQ)

25M: 1 lane x 9 swaths x 10 tiles = total of 90 tiles imaged.

![](/files/mZjsKdhwlRGJlcWChCRo)

50M: 2 lanes x 9 swaths x 10 tiles = total of 180 tiles imaged.

![](/files/7TbgUr3yVZ3GnmUY9yCo)

100M: 4 lanes x 9 swaths x 10 tiles = total of 360 tiles imaged.

![](/files/aTj3es1jxw36mVYlGIrK)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9348), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009348%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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